2022-10-23

Introduction

Study

Henrick et al. 2021: Bifidobacteria-mediated immune system imprinting early in life

  • Investigation: The effects of bifidobacteria and HMO-utilization genes during the first months of life
  • Methods: Longitudinal systems immunology analysis combined with metagenomic profiling

Focus in this data analysis:

  • Shotgun metagenomic sequencing of longitudinal fecal samples of infants

Study design

Data

Two TSV files:

Methods

Tidying data

  • Bin data by weeks
    • For subplots: filter by ‘Vaginal’ or ‘C-section’ prior to binning
  • Drop NAs
  • Filter data for weeks and bacterial species
    • Bifido heat map data: keep baby ID
  • Remove data >24 weeks
  • Clean up names

Raw data

Family meta data

##    sample.id baby_id family_id gestational_age group sex
## 1 2600164312     360       167             280  Term   1
## 2 2600100341     162        69             278  Term   0
## 3 2600100455     285       140             273  Term   0
##       mode_delivery Days_after_birth Month_of_life f__Methanobacteriaceae
## 1           Vaginal                0             0                      0
## 2 Planned_C-section                1             0                      0
## 3           Vaginal                1             0                      0
##   f__Actinomycetaceae f__Bifidobacteriaceae f__Candidatus_Nanopelagicaceae
## 1             0.03489               1.62129                              0
## 2             0.00188               0.42010                              0
## 3             0.00000               0.46499                              0

Raw data

Bifido meta data

##    sample.id baby_id family_id gestational_age group sex
## 1 2600164312     360       167             280  Term   1
## 2 2600100341     162        69             278  Term   0
## 3 2600100455     285       140             273  Term   0
##       mode_delivery Days_after_birth Month_of_life g__Bifidobacterium
## 1           Vaginal                0             0            1.62129
## 2 Planned_C-section                1             0            0.42010
## 3           Vaginal                1             0            0.46499
##   g__Bifidobacterium.s__Bifidobacterium_adolescentis
## 1                                            0.02872
## 2                                            0.02965
## 3                                            0.00147

Tidying data

Family data:

##   weeks Methanobacteriaceae Actinomycetaceae Bifidobacteriaceae
## 1     1                   0          0.03489            1.62129
## 2     1                   0          0.00188            0.42010
## 3     1                   0          0.00000            0.46499
## 4     1                   0          0.00000            0.25688
## 5     1                   0          0.01905            1.01351

Bifido data:

##   weeks B_adolescentis B_angulatum B_animalis
## 1     1        0.02872           0    0.00000
## 2     1        0.02965           0    0.01920
## 3     1        0.00147           0    0.00000
## 4     1        0.04929           0    0.00000
## 5     1        0.02277           0    0.04185

Tidying data

Family vaginal data:

Filter for vaginal

##    sample.id baby_id family_id gestational_age group sex mode_delivery
## 1 2600164312     360       167             280  Term   1       Vaginal
## 2 2600100455     285       140             273  Term   0       Vaginal
## 3 2600100500      23        21             278  Term   0       Vaginal

Bin by weeks and clean-up

##   weeks Methanobacteriaceae Actinomycetaceae Bifidobacteriaceae
## 1     1                   0          0.03489            1.62129
## 2     1                   0          0.00000            0.46499
## 3     1                   0          0.00000            1.05293

Same steps were performed with filtering for C-section

Tidying data

Bifido C-section data:

Filter for C-section

##    sample.id baby_id family_id group sex     mode_delivery
## 1 2600100341     162        69  Term   0 Planned_C-section
## 2 2600100458     276       137  Term   1 Planned_C-section
## 3 2600100460     270       135  Term   0 Planned_C-section

Bin by weeks and clean-up

##   weeks B_adolescentis B_angulatum B_animalis
## 1     1        0.02965           0    0.01920
## 2     1        0.04929           0    0.00000
## 3     1        0.02277           0    0.04185

Same steps were performed with filtering for Vaginal

Tidying data

Bifido heatmap data: Keeping baby ID when binning

##    weeks baby_id g__Bifidobacterium B_adolescentis
## 1      1     360            1.62129        0.02872
## 2      1     162            0.42010        0.02965
## 3      1     285            0.46499        0.00147
## 4      1     276            0.25688        0.04929
## 5      1     270            1.01351        0.02277
## 6      1     174           95.79804        0.00000
## 7      1     147           23.07769        0.00000
## 8      1     138            0.30136        0.13661
## 9      1      23            1.05293        0.00159
## 10     1     382            0.00000        0.00000

Data analysis

Exploring the data:

  • Change in gutmicrobes across 24 weeks
  • Family level abundance
  • Bifidobacterium species level abundance
  • Bifidobacterium species level abundance by baby ID

Results

Family level abundance

Calculating the relative abundance at family level. Families with mean ≤ 2% were merged into ‘Other’

Family level abundance

Splitting the previous plot into Vaginal and C-section births

Bifido sp. level abundance

Calculating the relative abundance at Bifidobacterium species level. Species with mean ≤ 2% were merged into ‘Other’

Bifido sp. level abundance

Splitting the previous plot into Vaginal and C-section births

Bifido species across infants

Bifido species across infants

Discussion

Discussion

  • Increase in Bacteroidaceae and Bifidobacteriaceae at family level after birth in the majority of newborns.
  • This expansion most frequently involved B. longum, B. breve, and B. bifidum in the first week.
  • Variation at family and bifidobacterium level between modes of birth
  • Highly variable bifidobacterial expansion across infants

Impact?

  • Potential to alter the trajectory of immune system development?